Description Usage Arguments Details Value See Also Examples
DataFrameQuantitativeTrack
creates and IGV
track for bed objects imported using rtracklayer
1 2 3 4 5 6 7 8 9 10 | DataFrameQuantitativeTrack(
trackName,
quantitativeData,
color = "blue",
trackHeight = 50,
autoscale,
min = NA_real_,
max = NA_real_,
visibilityWindow = 1e+05
)
|
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
quantitativeData |
A base R |
color |
A CSS color name (e.g., "red" or "#FF0000") |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
autoscale |
Autoscale track to maximum value in view |
min |
Sets the minimum value for the data (y-axis) scale. Usually zero. |
max |
Sets the maximum value for the data (y-axis) scale. This value is ignored if autoscale is TRUE |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
Detailed description goes here
A DataFrameQuantitativeTrack object
DataFrameAnnotationTrack
GRangesQuantitativeTrack
GRangesAnnotationTrack
DataFrameAnnotationTrack
DataFrameQuantitativeTrack
GRangesAnnotationTrack
GRangesQuantitativeTrack
GenomicAlignmentTrack
UCSCBedAnnotationTrack
UCSCBedGraphQuantitativeTrack
VariantTrack
igvAnnotationTrack
1 2 3 4 5 6 7 8 | base.loc <- 88883100
tbl <- data.frame(chrom=rep("chr5", 3),
start=c(base.loc, base.loc+100, base.loc + 250),
end=c(base.loc + 50, base.loc+120, base.loc+290),
score=runif(3),
stringsAsFactors=FALSE)
track <- DataFrameQuantitativeTrack("dataframeTest", tbl, autoscale=TRUE)
|
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